Table 2_Genetic variation in storage protein and starch biosynthesis genes reveals key associations with seed composition in pea (Pisum sativum).xlsx

Understanding the genetic basis of seed storage proteins and starch biosynthesis in pea (Pisum sativum) is critical for breeding programs aimed at enhancing seed quality, functional properties and nutritional value. In this study, we selected 34 genes encoding storage proteins and 21 genes involved in starch synthesis through literature mining and BLAST analysis. Using these genes as references, we sequenced 64 genomic regions associated with storage proteins and starch metabolic enzymes in 100 genetically diverse global pea accessions. In addition, protein and starch content analysis was conducted for these pea accessions. Targeted sequencing of these genes yielded 8,793 genetic variants, of which 2,573 high-quality single nucleotide polymorphism (SNP) markers were retained for further analysis. Protein content of studied accessions ranged from 19.5 to 37.7%, and starch content from 23.8 to 47.3%, highlighting the substantial phenotypic variation. Furthermore, a strong negative correlation (r = –0.71, p < 0.001) was observed between seed wrinkling and starch content consistent with the documented role of genetic variation in starch biosynthesis in determining seed texture. The SNP-based population structure and genetic diversity assessments revealed a complex genetic landscape with no clear clustering by geographical origin or material types. However, dendrograms constructed from principal components derived from SNP markers revealed a clear clustering of accessions according to their protein and starch content, thereby validating the influence of variants in the targeted genes on these traits. Gene-to-phenotype regression analysis identified key genes significantly associated with protein and starch content including legumin, provicilin and starch-branching enzyme. These findings provide valuable insights into the genetic architecture of storage protein and starch biosynthesis in pea and offer a foundation for targeted breeding strategies aimed at improving seed composition and functional properties.

解析豌豆（Pisum sativum）种子贮藏蛋白与淀粉生物合成的遗传基础，对于旨在提升种子品质、功能特性与营养价值的育种项目至关重要。本研究通过文献挖掘与BLAST分析，筛选得到34个编码贮藏蛋白的基因以及21个参与淀粉合成的基因。以这些基因为参照，我们对100份遗传多样性丰富的全球豌豆种质的64个与贮藏蛋白、淀粉代谢酶相关的基因组区域进行了靶向测序。此外，本研究还对供试豌豆种质的蛋白质与淀粉含量开展了测定分析。本次靶向测序共获得8793个遗传变异，其中保留2573个高质量单核苷酸多态性（single nucleotide polymorphism, SNP）标记用于后续分析。供试种质的蛋白质含量范围为19.5%至37.7%，淀粉含量范围为23.8%至47.3%，体现出显著的表型变异。此外，本研究观察到种子皱缩与淀粉含量之间存在极强的负相关关系（r = –0.71，p < 0.001），这与已有报道中淀粉生物合成遗传变异决定种子质地的结论一致。基于SNP标记的群体结构与遗传多样性分析揭示了复杂的遗传格局，未观察到明显的按地理来源或材料类型的聚类现象。但基于SNP标记主成分分析构建的系统发育树显示，供试种质可按照其蛋白质与淀粉含量进行清晰聚类，从而验证了靶向基因变异对这些性状的调控作用。基因-表型回归分析鉴定出与蛋白质和淀粉含量显著相关的关键基因，包括豆球蛋白（legumin）、前豌豆球蛋白（provicilin）以及淀粉分支酶（starch-branching enzyme）。本研究结果为解析豌豆贮藏蛋白与淀粉生物合成的遗传结构提供了重要见解，并为旨在优化种子组分与功能特性的靶向育种策略奠定了坚实基础。